Josh: If you merely mean carrying out MD with Amber of a protein
embedded in a lipid bilayer, goto J Chem Inf Model 2009, 49, 972,
where you can find ref to previous works. In short, VMD plugins are
used to prepare the membrane, while parameterization of the lipid is
carried out with antechamber, i.e., Amber world. If not relevant to
what you are looking for, beg pardon for the digression.
cheers
fp
On Sat, Oct 23, 2010 at 7:30 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Josh,
>
>> While our lab generally uses NAMD for our simulations of transmembrane
>> proteins, we are interested in testing out Amber11 on a Nvidia GPU using
> the
>> Charmm class of force-fields. Searching through the list archive, there
> are
>> several posts suggesting issues with Amber's ability to handle membrane
>> simulations. I was hoping that members of the list with experience in
>
> Most of these issues surround the fact that AMBER traditionally has never
> had a good force field for lipids. Work is in progress to correct this but
> for now this situation still exists. However, the program Chamber now lets
> you convert charmm psf and coord files to AMBER prmtop and inpcrd files.
> This lets you use the charmm force field for lipids and so should make such
> simulations easier.
>
> You will need to convert your psf from NAMD from an XPLOR format psf to a
> CHARMM one but that is fairly simple. Just run it through charmm and have it
> read and then write. At some point we will update chamber to support XPLOR
> format but that is in the future.
>
>> simulating protein/membrane systems using Amber could comment on
>> potential pitfalls moving a membrane system from NAMD to Amber.
>> Obviously the barostats are different, and it seems like NAMD allows
>> additional pressure controls absent in Amber. Additionally, if we are
> using
>
> The barostat should not cause any problems, just use anisotropic pressure
> scaling. You are correct that AMBER does not allow things like constant
> surface tension that a lot of people use for membranes but this is just
> hokey anyway since such an ensemble does not really exist. What is really
> needed are force fields that don't rely on such hacks to work correctly.
>
> You are probably best trying the latest Charmm lipid force field. I'm not
> sure how mature this is right now but it has been developed to work
> correctly with standard NPT ensembles. This should work with Chamber to
> allow one to run it in sander and pmemd, although I have heard of some
> people seeing issues with chamber when attempting this. These should be easy
> to fix but I'm still waiting on example input files to reproduce this.
>
>> the same force-field (charmm 27 w/CMAP corrections) that we used in
>> NAMD, is it safe to transfer the coordinates of our pre-equilibrated
> system
>> (from previous runs in NAMD) in a hexagonal cell to Amber, do a brief
>> minimization and heating and then start a production run, or would you
>> recommend rebuilding the system from scratch and doing a multi-tiered
>> restrained equilibration?
>
> What you describe, minimize, heat, should work fine. The only real issue is
> that at present chamber, I believe, only supports orthorhombic boxes. You
> might want to consider converting your water box to orthorhombic.
> Alternatively one could probably run it through and then modify the box
> dimensions and angles at the end of the inpcrd file. This might take some
> tweaking but could work. Mark can probably chime in here with details for
> using chamber on truncated octahedral boxes.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Sat Oct 23 2010 - 11:00:04 PDT
